There's an example for looking at a proton transfer using steered MD (you
can also use umbrella sampling, etc.) for a QM/MM potential on the Amber
tutorial website. (Advanced Tutorial 10)
http://ambermd.org/tutorials/advanced/tutorial10/
You typically need some type of biasing potential (like for umbrella
sampling or steered MD) to drive the reaction forward, which means that you
need some kind of definition or guess for the reaction coordinate. This is
caused by the fact that bond breaking typically has a large energy barrier
that makes it intractable to the (shortened) simulation time accessible via
QM/MM calculations.
HTH,
Jason
On Sun, Feb 12, 2012 at 1:38 PM, amir abbasi <amir-abbasi.hotmail.com>wrote:
>
> How To do bond breaking simulations with QM/MM?
> Is there any tutorials?
> Amber manual in not helpful in detail.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 12 2012 - 13:30:02 PST
